Bolt won the 200-meter event with a time of 20.29 at the Adidas Grand Prix meet Saturday at Icahn Stadium in Randall's Island, N.Y., where he broke the world record in the 100-meter for the first time in 2008.
Zharnel Hughes of Anguilla nearly edged Bolt as he finished the race with a time of 20.32, pointing to the track star and smiling after the finish.
Bolt, on the other hand, wasn't pleased with his performance despite the win.
"I'm not overly happy with it," Bolt said after the race. "The first 100 meters was poor, it was really bad.... I had to keep pushing myself."
Bolt last ran the 200 in May at the IAAF World Challenge in Ostrava, Czech Republic, where he posted a time of 20.13 after missing most of the 2014 season because of injury.
The Jamaican-born Bolt has won six Olympic gold medals and holds the world records in the 100 (9.58) and 200 meters (19.19).
"I have to figure out what I'm doing wrong, what I need to do to be better," Bolt said, looking forward to the 2016 Olympics in Rio de Janiero. "So right now I have to go back to the drawing board, figure out what's going on and get it done."
Bolt is set to race at the Paris and Lausanne, Switzerland, meets before the IAAF World Championships in Beijing in August, where he will go head to head with Gatlin for the first time this year.
"When I get to Beijing I'll be ready to go and that's when the showdown will be," Bolt told the BBC before competing Saturday.
Earlier in the day,
Lolo Jones, the Summer and Winter Olympian, ran the 110-meter hurdles in 12.95 seconds for fourth place, behind the winner, Sharika Nelvis of the United States, who finished with a 12.65.
Former New York Giants running back David Wilson made his professional track debut Saturday in the triple jump, though he finished ninth after his best jump of 14.66 meters.